Supporting data for "Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis"

Dataset type: Genomic
Data released on September 14, 2018

Gong G; Dan C; Xiao S; Guo W; Huang P; Xiong Y; Wu J; He Y; Zhang J; Li X; Chen N; Gui J; Mei J (2018): Supporting data for "Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis" GigaScience Database. http://dx.doi.org/10.5524/100506

DOI10.5524/100506

The yellow catfish, Pelteobagrus fulvidraco, belonging to Siluriformes order, is an important economic freshwater aquaculture fish species in Asia, especially in south China. Recently, the aquaculture industry is facing tremendous challenges in germplasm degeneration and poor diseases resistance. Meanwhile, yellow catfish exhibits notable sex dimorphism on growth rate that adult males are about two to three fold bigger than females. How aquaculture industry takes advantage of such sex dimorphism is another challenge. To address these challenges, a high-quality reference genome of the yellow catfish is needed. To construct a high-quality reference genome for yellow catfish, we generated 51.2 Gb short reads and 38.9 Gb long reads using Illumina and PacBio platforms, respectively. The sequencing data were assembled into 732.8 Mb genome assembly with contig N50 length of 1.1 Mb. Additionally, we applied Hi-C technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with 26 chromosomes, and a scaffold N50 length of 25.8 Mb. Using 24,552 protein-coding genes annotated in yellow catfish genome, the phylogenetic relationships of the yellow catfish with other teleosts showed that yellow catfish separated from the common ancestor of channel catfish ~81.9 million years ago. 1,717 gene families were identified to be expanded in yellow catfish and those gene families are mainly enriched in immune system, signal transduction, glycosphingolipid biosynthesis and fatty acid biosynthesis. Taking advantage of Illumina, PacBio and Hi-C technologies, we constructed the first high-quality chromosomal-level genome assembly for the yellow catfish P. fulvidraco. The genomic resources generated in this work not only offered valuable reference genome for functional genomics studies of yellow catfish to decipher the economic traits and sex determination, but also provided important chromosome information for genome comparisons in broad evolutionary research community.

Additional details

Read the peer-reviewed publication(s):

Gong, G., Dan, C., Xiao, S., Guo, W., Huang, P., Xiong, Y., … Mei, J. (2018). Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis. GigaScience. doi:10.1093/gigascience/giy120

Additional information:

http://www.biosino.org/node/project/detail/OEP000129

Accessions (data included in GigaDB):

PROJECT: PRJNA275380
PROJECT: PRJNA489116





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
OES013265 1234273 yellow catfishTachysurus fulvidraco Description:DNA extracted from muscle tissue of a ...
Alternative names:Pelteobagrus fulvidraco
Alternative accession-BioSample:SAMN09948750
...
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OES013266 1234273 yellow catfishTachysurus fulvidraco Description:Chromatin extracted from blood tissue ...
Alternative names:Pelteobagrus fulvidraco
Alternative accession-BioSample:SAMN09949663
...
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SAMN033439851234273 yellow catfishTachysurus fulvidraco Description:RNA extracted from gonad of a yellow c...
Alternative names:Pelteobagrus fulvidraco
Alternative accession-BioSample:SAMN03343985
...
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Displaying 1-3 of 3 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
otherTEXT0.69 KB2018-09-12
otherTSV251.88 KB2018-09-12
Coding SequenceFASTA36.58 MB2018-09-12
otherUNKNOWN4.92 MB2018-09-12
annotationGFF40.19 MB2018-09-12
Sequence assemblyFASTA705.95 MB2018-09-12
annotationGFF98.81 KB2018-09-12
Phylogenetic treeUNKNOWN0.59 KB2018-09-12
protein sequenceFASTA13.13 MB2018-09-12
SNPsVCF283.14 MB2018-09-12
Displaying 1-10 of 16 File(s).
Funding body Awardee Award ID Comments
Ministry of Agriculture and Rural Affairs of the People's Republic of China J Mei CARS-46 China Agriculture Research System
Ministry of Education of the People's Republic of China J Mei 2662017PY013 Fundamental Research Funds for the Central Universities
Date Action
September 14, 2018 Dataset publish
November 3, 2018 Manuscript Link added : 10.1093/gigascience/giy120